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- PDB-3uxj: Crystal Structure of 7-cyano-7-deazaguanine reductase, QueF from ... -

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Basic information

Entry
Database: PDB / ID: 3uxj
TitleCrystal Structure of 7-cyano-7-deazaguanine reductase, QueF from Vibrio cholerae complexed with NADP and PreQ0
ComponentsNADPH-dependent 7-cyano-7-deazaguanine reductase
KeywordsOxidoreductase/Oxidoreductase Substrate / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / alpha-beta structure / tunneling fold / reductase / cytosol / Oxidoreductase-Oxidoreductase Substrate complex
Function / homology
Function and homology information


preQ1 synthase / preQ1 synthase activity / tRNA modification / tRNA queuosine(34) biosynthetic process / cytosol / cytoplasm
Similarity search - Function
NADPH-dependent 7-cyano-7-deazaguanine reductase, QueF type 2 / NADPH-dependent 7-cyano-7-deazaguanine reductase, N-terminal / Nitrile reductase, 7-cyano-7-deazaguanine-reductase N-term / NADPH-dependent 7-cyano-7-deazaguanine reductase QueF / : / QueF-like protein / GTP Cyclohydrolase I, domain 2 / GTP cyclohydrolase I, C-terminal domain/NADPH-dependent 7-cyano-7-deazaguanine reductase, N-terminal domain / GTP cyclohydrolase I, C-terminal/NADPH-dependent 7-cyano-7-deazaguanine reductase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 7-DEAZA-7-AMINOMETHYL-GUANINE / NADPH-dependent 7-cyano-7-deazaguanine reductase / NADPH-dependent 7-cyano-7-deazaguanine reductase
Similarity search - Component
Biological speciesVibrio cholerae O1 biovar El Tor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.401 Å
AuthorsKim, Y. / Zhang, R. / Gu, M. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published / Year: 2012
Title: Crystal Structure of 7-cyano-7-deazaguanine reductase, QueF from Vibrio cholerae complexed with NADP and PreQ0
Authors: Kim, Y. / Zhang, R. / Gu, M. / Anderson, W.F. / Joachimiak, A. / CSGID
History
DepositionDec 5, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 4, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NADPH-dependent 7-cyano-7-deazaguanine reductase
B: NADPH-dependent 7-cyano-7-deazaguanine reductase
C: NADPH-dependent 7-cyano-7-deazaguanine reductase
D: NADPH-dependent 7-cyano-7-deazaguanine reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,84719
Polymers133,0854
Non-polymers2,76215
Water20,0331112
1
A: NADPH-dependent 7-cyano-7-deazaguanine reductase
B: NADPH-dependent 7-cyano-7-deazaguanine reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,07912
Polymers66,5432
Non-polymers1,53610
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7250 Å2
ΔGint10 kcal/mol
Surface area19870 Å2
MethodPISA
2
C: NADPH-dependent 7-cyano-7-deazaguanine reductase
D: NADPH-dependent 7-cyano-7-deazaguanine reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,7687
Polymers66,5432
Non-polymers1,2265
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6500 Å2
ΔGint4 kcal/mol
Surface area20020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.387, 71.416, 71.358
Angle α, β, γ (deg.)110.01, 119.54, 99.46
Int Tables number1
Space group name H-MP1
Detailstwo dimers, chains A and B, and chains C and D.

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Components

#1: Protein
NADPH-dependent 7-cyano-7-deazaguanine reductase / 7-cyano-7-carbaguanine reductase / NADPH-dependent nitrile oxidoreductase / PreQ(0) reductase


Mass: 33271.285 Da / Num. of mol.: 4 / Mutation: R262L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae O1 biovar El Tor (bacteria)
Strain: N16961 / Gene: queF, VCM66_0859 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic
References: UniProt: C3LTF1, UniProt: Q9KTK0*PLUS, preQ1 synthase
#2: Chemical
ChemComp-PRF / 7-DEAZA-7-AMINOMETHYL-GUANINE


Mass: 179.179 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H9N5O
#3: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1112 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsTHE PREQ0 COMPOUND REACTED SO THAT A COVALENT BOND WAS FORMED BETWEEN THE COMPOUND (REPRESENTED AS ...THE PREQ0 COMPOUND REACTED SO THAT A COVALENT BOND WAS FORMED BETWEEN THE COMPOUND (REPRESENTED AS PRF) AND CYS 194. AUTHORS STATE THAT THE COMPLEX IS SUPPOSED TO BE A TRANSITION STATE INTERMEDIATE TRAPPED BY MUTATION. THE C10 ATOM OF PRF IS MORE CLOSE TO SP2 BUT NOT NECESSARILY 100%. IT IS FLAT IN SPITE OF STERIC HINDRANCE AND ACTUALLY SLIGHTLY OFF FROM THE FLAT, BETWEEN SP2 AND SP3. THE BOND BETWEEN C10 OF PRF AND SG OF CYS SHOULD BE PARTIAL DOUBLE BOND.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.04 Å3/Da / Density % sol: 39.73 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 0.2 M sodium chloride, 0.1 M sodium potassium phosphate pH 6.2, 20 % (w/v) PEG-1000, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97903 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Dec 18, 2010 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97903 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. all: 194723 / Num. obs: 194723 / % possible obs: 94.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Biso Wilson estimate: 10.85 Å2 / Rsym value: 0.026 / Net I/σ(I): 17.6
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 5 / Num. unique all: 6903 / Rsym value: 0.139 / % possible all: 67.1

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
MOLREPphasing
PHENIX(phenix.refine: 1.7.3_920)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3S19

3s19


Resolution: 1.401→27.009 Å / SU ML: 0.17 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 14.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.165 9810 5.04 %random
Rwork0.132 ---
all0.134 194705 --
obs0.134 194705 94.09 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.887 Å2 / ksol: 0.39 e/Å3
Displacement parametersBiso mean: 14.2 Å2
Baniso -1Baniso -2Baniso -3
1-0.5345 Å2-0.7416 Å2-0.3987 Å2
2---1.284 Å2-1.9309 Å2
3---0.7494 Å2
Refinement stepCycle: LAST / Resolution: 1.401→27.009 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8342 0 166 1112 9620
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0189416
X-RAY DIFFRACTIONf_angle_d1.84412925
X-RAY DIFFRACTIONf_dihedral_angle_d17.1443542
X-RAY DIFFRACTIONf_chiral_restr0.1351373
X-RAY DIFFRACTIONf_plane_restr0.011749
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.4007-1.41660.22512220.18624223444565
1.4166-1.43330.21342710.18044766503773
1.4333-1.45080.23432920.17885636592886
1.4508-1.46910.20283040.16416107641193
1.4691-1.48850.20113170.15796240655793
1.4885-1.50880.20853290.14486045637494
1.5088-1.53040.17683510.12526234658595
1.5304-1.55320.16353180.12146288660695
1.5532-1.57750.18993390.11586099643895
1.5775-1.60340.15543610.10586180654195
1.6034-1.6310.15323420.10866245658795
1.631-1.66070.16193640.11156259662395
1.6607-1.69260.16023350.1096213654895
1.6926-1.72710.16373450.10426279662496
1.7271-1.76470.13983260.10316222654896
1.7647-1.80570.15883090.10516317662696
1.8057-1.85090.14463170.11016338665596
1.8509-1.90090.16013430.11416298664196
1.9009-1.95680.15383710.11546339671097
1.9568-2.020.15883150.11836361667697
2.02-2.09210.17033390.13166431677097
2.0921-2.17590.15453500.13136310666097
2.1759-2.27490.16483220.12956357667997
2.2749-2.39470.16633190.1296453677298
2.3947-2.54460.15343150.13666454676998
2.5446-2.74090.17823240.1426437676198
2.7409-3.01650.18783310.1516419675098
3.0165-3.45220.1553470.1376481682899
3.4522-4.34640.13873240.12926487681199
4.3464-27.01430.16823680.16046377674598

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